Calcium in PDB 6oqq: Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex
Protein crystallography data
The structure of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex, PDB code: 6oqq
was solved by
D.R.Tomchick,
V.S.Tagliabracci,
M.Black,
A.Osinski,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.83 /
2.10
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
105.490,
104.749,
107.770,
90.00,
103.97,
90.00
|
R / Rfree (%)
|
20.2 /
23.4
|
Other elements in 6oqq:
The structure of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex
(pdb code 6oqq). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex, PDB code: 6oqq:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 6oqq
Go back to
Calcium Binding Sites List in 6oqq
Calcium binding site 1 out
of 4 in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca201
b:55.8
occ:1.00
|
OD1
|
B:ASN25
|
2.2
|
32.3
|
1.0
|
O
|
B:HOH321
|
2.2
|
46.0
|
1.0
|
OD1
|
B:ASP23
|
2.3
|
43.0
|
1.0
|
O
|
B:SER27
|
2.3
|
27.4
|
1.0
|
OD1
|
B:ASP21
|
2.4
|
26.5
|
1.0
|
CG
|
B:ASN25
|
2.9
|
31.8
|
1.0
|
H
|
B:ASN25
|
3.0
|
31.2
|
1.0
|
H
|
B:SER27
|
3.1
|
31.0
|
1.0
|
HD21
|
B:ASN25
|
3.2
|
47.6
|
1.0
|
ND2
|
B:ASN25
|
3.4
|
39.6
|
1.0
|
CG
|
B:ASP23
|
3.4
|
29.2
|
1.0
|
CG
|
B:ASP21
|
3.5
|
26.2
|
1.0
|
C
|
B:SER27
|
3.5
|
26.9
|
1.0
|
HG
|
B:SER27
|
3.6
|
36.8
|
1.0
|
H
|
B:ASP23
|
3.7
|
65.6
|
1.0
|
N
|
B:ASN25
|
3.8
|
26.1
|
1.0
|
H
|
B:ASN24
|
3.8
|
42.1
|
1.0
|
HA
|
B:ASP21
|
3.8
|
32.8
|
1.0
|
OD2
|
B:ASP23
|
3.9
|
41.0
|
1.0
|
N
|
B:SER27
|
3.9
|
26.0
|
1.0
|
HA
|
B:ILE28
|
4.0
|
33.7
|
1.0
|
CB
|
B:ASN25
|
4.1
|
26.7
|
1.0
|
OG
|
B:SER27
|
4.1
|
30.6
|
1.0
|
H
|
B:GLY26
|
4.1
|
30.3
|
1.0
|
HD22
|
B:ASN25
|
4.1
|
47.6
|
1.0
|
N
|
B:ASN24
|
4.2
|
35.0
|
1.0
|
OE1
|
B:GLN63
|
4.2
|
73.8
|
1.0
|
OD2
|
B:ASP21
|
4.2
|
25.9
|
1.0
|
CA
|
B:SER27
|
4.3
|
26.7
|
1.0
|
HB3
|
B:ASN25
|
4.3
|
31.9
|
1.0
|
CA
|
B:ASN25
|
4.3
|
25.9
|
1.0
|
N
|
B:ASP23
|
4.4
|
54.6
|
1.0
|
H
|
B:LYS22
|
4.4
|
79.3
|
1.0
|
CA
|
B:ASP21
|
4.4
|
27.4
|
1.0
|
CB
|
B:ASP21
|
4.4
|
26.7
|
1.0
|
N
|
B:GLY26
|
4.5
|
25.4
|
1.0
|
N
|
B:ILE28
|
4.6
|
47.9
|
1.0
|
C
|
B:ASP21
|
4.6
|
28.1
|
1.0
|
C
|
B:ASP23
|
4.6
|
28.4
|
1.0
|
N
|
B:LYS22
|
4.6
|
66.0
|
1.0
|
C
|
B:ASN25
|
4.6
|
25.6
|
1.0
|
HB2
|
B:ASP21
|
4.7
|
31.9
|
1.0
|
O
|
B:HOH327
|
4.7
|
47.5
|
1.0
|
CB
|
B:ASP23
|
4.7
|
37.6
|
1.0
|
CA
|
B:ILE28
|
4.8
|
28.2
|
1.0
|
CA
|
B:ASP23
|
4.8
|
39.8
|
1.0
|
HA
|
B:ASN24
|
4.8
|
32.9
|
1.0
|
C
|
B:ASN24
|
4.8
|
26.8
|
1.0
|
CB
|
B:SER27
|
4.8
|
27.5
|
1.0
|
CA
|
B:ASN24
|
4.9
|
27.4
|
1.0
|
HB2
|
B:ASN25
|
4.9
|
31.9
|
1.0
|
|
Calcium binding site 2 out
of 4 in 6oqq
Go back to
Calcium Binding Sites List in 6oqq
Calcium binding site 2 out
of 4 in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca202
b:0.8
occ:1.00
|
OD1
|
B:ASP94
|
2.3
|
63.6
|
1.0
|
OD1
|
B:ASN96
|
2.4
|
97.5
|
1.0
|
O
|
B:LEU100
|
2.4
|
64.7
|
1.0
|
OD1
|
B:ASP98
|
2.6
|
78.5
|
1.0
|
CG
|
B:ASN96
|
3.2
|
0.3
|
1.0
|
HA
|
B:ASP94
|
3.4
|
73.4
|
1.0
|
CG
|
B:ASP98
|
3.4
|
79.4
|
1.0
|
CG
|
B:ASP94
|
3.5
|
77.7
|
1.0
|
HD21
|
B:ASN96
|
3.6
|
0.5
|
1.0
|
H
|
B:ASP98
|
3.7
|
98.5
|
1.0
|
C
|
B:LEU100
|
3.7
|
66.0
|
1.0
|
H
|
B:LEU100
|
3.7
|
76.8
|
1.0
|
OD2
|
B:ASP98
|
3.7
|
80.1
|
1.0
|
H
|
B:ASN96
|
3.7
|
0.0
|
1.0
|
ND2
|
B:ASN96
|
3.8
|
94.6
|
1.0
|
H
|
B:GLY97
|
3.9
|
0.3
|
1.0
|
HA
|
B:ILE101
|
3.9
|
92.3
|
1.0
|
CA
|
B:ASP94
|
4.1
|
61.1
|
1.0
|
H
|
B:LYS95
|
4.1
|
0.9
|
1.0
|
CB
|
B:ASP94
|
4.1
|
63.9
|
1.0
|
HB2
|
B:ASP94
|
4.1
|
76.7
|
1.0
|
HB2
|
B:LEU100
|
4.2
|
84.6
|
1.0
|
HB3
|
B:ASN96
|
4.3
|
0.4
|
1.0
|
CB
|
B:ASN96
|
4.3
|
97.0
|
1.0
|
N
|
B:LEU100
|
4.3
|
64.0
|
1.0
|
N
|
B:ASN96
|
4.4
|
86.7
|
1.0
|
N
|
B:ASP98
|
4.4
|
82.0
|
1.0
|
N
|
B:LYS95
|
4.5
|
89.9
|
1.0
|
OD2
|
B:ASP94
|
4.5
|
72.6
|
1.0
|
CA
|
B:LEU100
|
4.5
|
66.4
|
1.0
|
N
|
B:GLY97
|
4.5
|
91.1
|
1.0
|
H
|
B:GLY99
|
4.5
|
84.5
|
1.0
|
C
|
B:ASP94
|
4.5
|
65.6
|
1.0
|
HD22
|
B:ASN96
|
4.6
|
0.5
|
1.0
|
CB
|
B:ASP98
|
4.6
|
81.9
|
1.0
|
N
|
B:ILE101
|
4.6
|
72.2
|
1.0
|
HB3
|
B:ASP98
|
4.7
|
98.4
|
1.0
|
CA
|
B:ILE101
|
4.7
|
76.9
|
1.0
|
CA
|
B:ASN96
|
4.8
|
98.3
|
1.0
|
CB
|
B:LEU100
|
4.8
|
70.5
|
1.0
|
HG23
|
B:ILE101
|
5.0
|
75.3
|
1.0
|
N
|
B:GLY99
|
5.0
|
70.3
|
1.0
|
|
Calcium binding site 3 out
of 4 in 6oqq
Go back to
Calcium Binding Sites List in 6oqq
Calcium binding site 3 out
of 4 in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca201
b:81.5
occ:1.00
|
O
|
D:SER27
|
2.2
|
69.2
|
1.0
|
OD1
|
D:ASP23
|
2.3
|
77.4
|
1.0
|
OD1
|
D:ASN25
|
2.6
|
60.0
|
1.0
|
OD1
|
D:ASP21
|
2.6
|
59.6
|
1.0
|
HD21
|
D:ASN25
|
2.9
|
78.7
|
1.0
|
CG
|
D:ASP23
|
3.2
|
68.5
|
1.0
|
CG
|
D:ASN25
|
3.2
|
60.2
|
1.0
|
H
|
D:SER27
|
3.2
|
73.3
|
1.0
|
ND2
|
D:ASN25
|
3.3
|
65.5
|
1.0
|
C
|
D:SER27
|
3.3
|
62.3
|
1.0
|
OD2
|
D:ASP23
|
3.4
|
72.9
|
1.0
|
HG
|
D:SER27
|
3.5
|
83.5
|
1.0
|
HA
|
D:ASP21
|
3.6
|
71.4
|
1.0
|
H
|
D:ASN25
|
3.7
|
71.2
|
1.0
|
HA
|
D:ILE28
|
3.7
|
90.0
|
1.0
|
CG
|
D:ASP21
|
3.7
|
59.4
|
1.0
|
H
|
D:ASP23
|
3.9
|
75.5
|
1.0
|
OG
|
D:SER27
|
4.0
|
69.5
|
1.0
|
N
|
D:SER27
|
4.0
|
61.1
|
1.0
|
HD22
|
D:ASN25
|
4.1
|
78.7
|
1.0
|
CA
|
D:SER27
|
4.2
|
60.3
|
1.0
|
N
|
D:ILE28
|
4.3
|
89.2
|
1.0
|
CA
|
D:ASP21
|
4.3
|
59.6
|
1.0
|
H
|
D:ASN24
|
4.4
|
71.6
|
1.0
|
H
|
D:GLY26
|
4.4
|
70.9
|
1.0
|
CA
|
D:ILE28
|
4.4
|
75.0
|
1.0
|
N
|
D:ASN25
|
4.4
|
59.4
|
1.0
|
CB
|
D:ASP21
|
4.4
|
59.4
|
1.0
|
HB2
|
D:ASP21
|
4.5
|
71.1
|
1.0
|
CB
|
D:ASN25
|
4.5
|
60.6
|
1.0
|
HG2
|
D:GLN63
|
4.5
|
0.1
|
1.0
|
CB
|
D:ASP23
|
4.5
|
62.6
|
1.0
|
OD2
|
D:ASP21
|
4.6
|
59.1
|
1.0
|
H
|
D:SER29
|
4.6
|
79.9
|
1.0
|
H
|
D:LYS22
|
4.6
|
0.8
|
1.0
|
N
|
D:ASP23
|
4.7
|
62.9
|
1.0
|
CB
|
D:SER27
|
4.7
|
60.8
|
1.0
|
HB3
|
D:ASN25
|
4.7
|
72.7
|
1.0
|
C
|
D:ASP21
|
4.8
|
59.8
|
1.0
|
N
|
D:GLY26
|
4.8
|
59.2
|
1.0
|
N
|
D:ASN24
|
4.8
|
59.8
|
1.0
|
C
|
D:ILE28
|
4.8
|
81.4
|
1.0
|
HB3
|
D:ASP23
|
4.8
|
75.2
|
1.0
|
N
|
D:LYS22
|
4.9
|
89.8
|
1.0
|
N
|
D:SER29
|
4.9
|
66.6
|
1.0
|
CA
|
D:ASN25
|
4.9
|
59.4
|
1.0
|
|
Calcium binding site 4 out
of 4 in 6oqq
Go back to
Calcium Binding Sites List in 6oqq
Calcium binding site 4 out
of 4 in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca202
b:0.6
occ:1.00
|
HD21
|
D:ASN96
|
1.9
|
0.7
|
1.0
|
OD1
|
D:ASN96
|
2.4
|
0.7
|
1.0
|
ND2
|
D:ASN96
|
2.4
|
0.5
|
1.0
|
OD1
|
D:ASP94
|
2.6
|
89.5
|
1.0
|
O
|
D:LEU100
|
2.6
|
91.3
|
1.0
|
OD1
|
D:ASP98
|
2.7
|
0.1
|
1.0
|
CG
|
D:ASN96
|
2.7
|
0.3
|
1.0
|
OD2
|
D:ASP98
|
2.9
|
0.8
|
1.0
|
CG
|
D:ASP98
|
3.0
|
0.5
|
1.0
|
HD22
|
D:ASN96
|
3.2
|
0.7
|
1.0
|
H
|
D:ASN96
|
3.6
|
0.7
|
1.0
|
H
|
D:ASP98
|
3.6
|
0.9
|
1.0
|
H
|
D:LEU100
|
3.7
|
0.7
|
1.0
|
CG
|
D:ASP94
|
3.7
|
90.3
|
1.0
|
HB3
|
D:LEU100
|
3.7
|
0.4
|
1.0
|
H
|
D:GLY97
|
3.8
|
0.9
|
1.0
|
C
|
D:LEU100
|
3.8
|
96.2
|
1.0
|
HA
|
D:ASP94
|
3.9
|
0.2
|
1.0
|
CB
|
D:ASN96
|
4.2
|
0.4
|
1.0
|
H
|
D:LYS95
|
4.3
|
0.8
|
1.0
|
CB
|
D:ASP98
|
4.3
|
0.4
|
1.0
|
N
|
D:LEU100
|
4.3
|
0.1
|
1.0
|
HA
|
D:ILE101
|
4.3
|
0.2
|
1.0
|
N
|
D:ASN96
|
4.4
|
0.6
|
1.0
|
N
|
D:ASP98
|
4.4
|
0.1
|
1.0
|
OD2
|
D:ASP94
|
4.4
|
88.1
|
1.0
|
CA
|
D:LEU100
|
4.4
|
0.7
|
1.0
|
HB3
|
D:ASN96
|
4.5
|
0.9
|
1.0
|
HB3
|
D:ASP98
|
4.5
|
0.5
|
1.0
|
CB
|
D:LEU100
|
4.5
|
97.8
|
1.0
|
H
|
D:GLY99
|
4.5
|
0.4
|
1.0
|
N
|
D:GLY97
|
4.5
|
0.5
|
1.0
|
CA
|
D:ASP94
|
4.6
|
91.8
|
1.0
|
HG22
|
D:ILE101
|
4.6
|
99.8
|
1.0
|
CB
|
D:ASP94
|
4.6
|
93.8
|
1.0
|
N
|
D:LYS95
|
4.7
|
0.9
|
1.0
|
HD23
|
D:LEU100
|
4.7
|
0.4
|
1.0
|
HB2
|
D:ASN96
|
4.7
|
0.9
|
1.0
|
CA
|
D:ASN96
|
4.8
|
0.6
|
1.0
|
C
|
D:ASP94
|
4.8
|
85.1
|
1.0
|
N
|
D:ILE101
|
4.8
|
93.8
|
1.0
|
HB2
|
D:ASP94
|
4.9
|
0.6
|
1.0
|
CA
|
D:ASP98
|
4.9
|
0.8
|
1.0
|
N
|
D:GLY99
|
5.0
|
0.3
|
1.0
|
|
Reference:
M.H.Black,
A.Osinski,
M.Gradowski,
K.A.Servage,
K.Pawlowski,
D.R.Tomchick,
V.S.Tagliabracci.
Bacterial Pseudokinase Catalyzes Protein Polyglutamylation to Inhibit the Side-Family Ubiquitin Ligases. Science V. 364 787 2019.
ISSN: ESSN 1095-9203
PubMed: 31123136
DOI: 10.1126/SCIENCE.AAW7446
Page generated: Tue Jul 16 12:34:44 2024
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